Workshop: From first draft to article submission and data sharing:

tips and tricks for successful scientific publication

auspiciado por Springer Nature

Dr. Klaus Mehltreter Instituto de Ecología, A.C., Xalapa

kmehltreter@gmail.com

Presentation Dr. rer. nat. Klaus Mehltreter Biologist, Ecologist Researcher at Instituto de Ecología, A.C., Xalapa, Ver., Mexico Research interest: Fern Ecology Reviewer for 35 journals Associate Editor: American Fern Journal, Fern Gazette, Neotropical Naturalist Professor of postgradate course: “Redacción y publicacion científica en inglés” (since 2011)

Content • Reflections about writing • 23 steps from first draft to final acceptance • Short exercises • Tips

The need for scientific publication Unfortunately, the education and training of scientists are often so overwhelmingly committed to science that the communication arts are neglected or ignored. In short, many good scientists are poor writers. Certainly, many scientists do not like to write. (Day 1979)

English

• 5-9% of world population are native English speakers

• Ca. 80% of scientific articles pulbished in English

Montgomery, S. L. 2004. Does science need a global language ? English and the future of research. Chicago, University of Chicago Press.

Scientific Paper trail 2011

Nature 480, 426–429, 21 December 2011

Rank Country Docs Citable docs Citations

Self-citations

Citations per document H index

1 USA 601990 532297 740612 379873 1.23 1965 2 China 471472 458299 440673 283196 0.93 655 3 UK 182849 158513 248158 75417 1.36 1213 4 Germany 164242 149645 217379 72258 1.32 1059 5 India 138986 128760 89952 35652 0.65 478 6 Japan 121262 112645 109674 35182 0.9 871 7 France 112796 103637 144019 39266 1.28 966 8 Italy 105847 95078 140890 48796 1.33 839 9 Canada 96928 87466 127252 31159 1.31 963

10 Australia 89767 80133 123355 34527 1.37 795 11 Spain 85560 77829 106490 29013 1.24 723 12 South Korea 78660 75162 76386 21464 0.97 536 13 Russia 73207 70352 39337 18387 0.54 467 14 Brazil 68908 64850 55863 17913 0.81 461 15 Netherlands 55520 50349 93350 20387 1.68 835 16 Iran 49572 47390 47438 22989 0.96 234

…28 Mexico 21005 19564 16164 3980 0.77 352

Published doc per country 2016 (SCImago)

In Greek times, written manuscripts were not made to read, they were an aid to memorize facts and stories.

The beginnings

- no punctuation marks (first ca. 200 B. C.) - no lowercase letters - no spaces (became common 800 A.D.)

The Greek used “Scriptio continua” written on scrolls. Manuscripts needed to be read by speaking them aloud.

- no index - no page numbers

Email and chat do not necessarily amend our writing abilities

Hola Dr… le envió un cordial saludo antes que nada una disculpa me perdí un rato para lo del trabajo de xxxxxx en yyyyyyy, le escribo para decirle que aun sigue en pie el trabajo ya estoy iniciando con la materia de experiencia recepcionista para ya dar de alta mi trabajo y la documentación que piden en mi facultad, estuve trabajando en el protocolo el cual le envió espero pueda checarlo y darme sus puntos vista aun no salgo a campo no se me a autorizado; pero ya me dedico al trabajo estos meses atte zzzzzzz

Writing is easy. All you do is stare at a blank sheet of paper until drops of blood form on your forehead. G. Fowler

Tip: Assign some of your most productive time to write daily

Recommendation to read

“First and foremost, I urge you (the student) to stay on the path (of science) you have chosen, and to travel on it as far as you can. The world needs you – badly.” (Wilson, E.O. 2013: Letters to a young scientist. Liveright, New York. 244 pp.)

Step 0: Think before you write Never sit down to write before you have thought long enough and hard enough about your

1. research question, 2. experimental design, 3. data analyses (incl. statistics), and 4. read enough about your research area,

so that you can present and discuss your work logically and honestly. Writing is relatively easy to learn, if you have something to say. (adapted from Vaughan Payne 1965)

Step 1: Research question

• What is your research question? Never start a research without any specific aim. Avoid the strategy: “If I collect enough data, something interesting will show up.” • Curiosity driven • Based on own observations • Imposed by your boss or research leader • Found in the current literature

Step 1: Research question • What is a good research question?

• Do you have the necessary

– knowledge and experience (incl. your team)? – materials, tools (e.g., software)? – equipment (e.g., laboratory)? – budget (e.g., project funding)? – time (e.g., sholarship, deadlines)?

• Is the research innovative?

• Will you be able to answer the question with your

research? experimental design

Step 2: Experimental design • Observational studies • Experimental studies

• Get all the help you can find:

Ask senior researchers, Ph.D. and posdocs, lab technicians, colleagues, other students

• Write a draft for your methods section • Will the results allow you to answer your research

question? • If your experimental design is wrong, you risk to fail.

Step 3: Structure of your publication

Know the structure of your publication from the beginning: • Thesis: Look at former thesis at your

institutional library. • Scientific article: Read journals of your

research area and look at their structure.

Step 3: Structure of your publication

Typical structure of an original scientific contribution is IMRAD:

Introduction Methods Results And Discussion

Step 3: Structure of your publication Example for a original research paper: Title Authors with institutional adresses Abstract with keywords (key contributions, etc.) Introduction, Methods, Results And Discussion (Conclusion) Acknowledgments References (e.g. Literature cited) Tables Figure Legends Figures

Step 3: Structure of your publication Different formats apply to other scientific contributions: • Review article • Scientific notes • Letters to the editor • Scientific books • Book chapters • Technical manuals, handbooks, reference books • Project reports • Article for a Newspaper

Step 4: Agree preliminary authorship • Who will contribute? • What is the order of authors?

– First author – Corresponding author* – Last author

• Who does the research, experiments, data analysis and the writing?

Example: PhDStudent1, Labchief1*, Posdoc1, Labtechnician1, Labtechnician2,, InternationalCollaborator1, Studentadviser1, ResearchLeader1

• What is a good title? – True/Representative – Attractive/interesting – max. 12 words (without articles and prepositions;

APA, 2010)

• How can you we find the best title for your manuscript?

• Do journals with higher IF have better titles?

Step 5: Choose a preliminary title

Titles

• Simple: “Biogeography of the Dryopteris patula complex in South America”

• Composed title: “Studies on Dryopteris: biogeography of the D. patula complex in South America.”

• Questions: “Is the alcohol extract of Dryopteris carthusiana the cure of breast cancer?”

• Mini-Summary: “Alcohol extracts of Dryopteris carthusiana cure breast cancer.”

Tip: How to find the best title for your manuscript?

• Write down the current title of your manuscript.

• Think about three alternative titles and write them down.

• Choose the title, which is the best in your opinion. Explain it to yourself!

Good or bad titles? 3 examples Qualify the following three titles:

1. very good 2. good, but improvable 3. bad Do you know what the article is dealing with by reading the title? Is the title clear, informative and detailed, without being too long?

Good or bad titles?

1. Variation in formaldehyde removal efficiency among indoor plant species.

2. A note on pteridophytes of the Indravati Tiger Reserve, Dantewada, Chhattisgarh.

3. Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae).

Good or bad titles?

1. Variation in formaldehyde removal efficiency among indoor plant species. (IF: 0.688), Good, but improvable

2. A note on pteridophytes of the Indravati Tiger Reserve, Dantewada, Chhattisgarh. (no-ISI): Bad

3. Molecular phylogeny, character evolution, and biogeography of the grammitid fern genus Lellingeria (Polypodiaceae). (IF: 2.664), Very good

Step 6: Preparations before writing For whom do you write? Who will be interested in your research? Other scientists? Industry? General public? • Choose journal and obtain author guidelines What are your main research results? • You have finished data analysis and performed current statistics to back up your

results • You have designed clear tables and figures illustrating quickly your results • You have you original data organized, archived and accessible on your computer • You have read the most relevant literature in your field of research.

– You did background reading: general articles, review articles, and books. – You did specific reading: articles dealing with the same or related research questions – You have read current articles from your selected journal.

TIP: Know the journal for which you are writing!

Step 6: Preparations before writing How good is your research? Assess your work. Do an honest self-evaluation. • one more piece of basic knowledge: some new data on a characteristics of

a material • locally important • regionally important • of worldwide interest • useful for technical, agricultural, industrial applications • Groundbreaking, innovative research

Who are your coauthors and how will they contribute during writing? • Agree authorship • You have agreed on the chosen journal

Where do you start writing?

• 1. Introduction: What is already known about your research question? What question was studied?

• 2. Method: How were the studies performed? • 3. Results: What were the findings?, and • 4. Discussion: What do these findings mean?

• 5. Abstract: Short version of your manuscript

Step 7: Outline • Draft an outline of your manuscript • An outline is a collection of headings and

subheadings, which will help you – organizing the structure of your manuscript – staying focused and – keeping track of your writing.

• The draft also helps you to start over quickly after breaks and interruptions at work.

Step 7: Outline - Example

Example of an outline for an introduction Title: An invasive tree fern alters soil and plant nutrient dynamics in Hawaii

Introduction: 1. Tree ferns 2. Effects of tree ferns on ecosystems 3. Hawaii 4. The introduced tree fern Sphaeropteris cooperi

Chau et al. 2013: Biological

Invasions 15 (2): 355-370.

Step 7: Outline - Example 1. Tree ferns Nutrient acquisition and retention Leaf decomposition 2. Effects of tree ferns on ecosystems Competitive dominance Hosts for epiphytes Colonizers of disturbed habitats 3. Hawaii Susceptibility to invasions Introductions on the islands % introduced species becoming invasive Effect of invasive species 4. The introduced tree fern Sphaeropteris cooperi Introductions and current distribution Comparison with native tree fern species Litter effects of S. cooperi on other plants

Chau et al. 2013: Biological Invasions 15 (2): 355-370.

Step 7: Outline

• Draft as early as possible. Your ideas should be kept on paper. The largest part of your early versions will go into the trash, but they will help you to clarify your ideas and to improve the structure of your manuscript.

• Plan to rewrite your manuscripts at least three times and get some feedback by colleagues and coauthors each time before you rewrite the manuscript.

Step 8: Introduction • Short, concise, clear (typically 3-5 paragraphs) • Mostly written in present tense (referring to

established knowledge) • Has to catch the reader (where is the hook?) • Defines key terms • Raises problems, questions and controversies • Defends the need for this research • Presents most necessary background information • Has a good logical structure • Ends up with research questions, objectives of the

study or hypotheses

Step 9: Materials and Methods This section has to warrant that other researchers can reproduce your results if they use the same materials and follow the same methods • Concisely and clearly written in past tense (referring to your work) • If you have used common standard techniques and well-known

procedures, only cite a reference – Example: “We analyzed plant tissues for nitrogen content following standard techniques

(USDA 2013)”

• All specific details have to be described: – Experimental conditions (e.g., temperature, pressure) – Chemical materials used – Lab and field equipment – For field studies: describe study site (e.g., location, surrounding, vegetation) – For biological studies: describe study species and voucher material involved – Procedures involved and techniques applied

• Focus on your main results – Do not report all your results, even if irrelevant for your

contribution. • Concisely and clearly written in past tense (referring to your

work) • Do not be anecdotal:

– “We repeated the data analysis because we had a nasty virus on our computer.”

• Only report results of your research – Do not discuss results in this section (unless the journal allows

for a joint section of Results and Discussion) • Use figures and tables whenever data are complex • Do not repeat results in text and graphs

Step 10: Results

TIP: Be organized! You do not want to rewrite your results several times because you analyzed the erroneous data files.

The discussion should respond all questions raised in the introduction, and clarify which hypotheses were confirmed or rejected. It is the most difficult section to write, and typically it is longer than the results section.

• Do not recapitulate your results. • Concisely and clearly written in present tense (referring to established

knowledge) and in past tense (referring to your work) • Present the relationships and generalizations backed up by your results. • Compare your results with other studies • Point out important coincidences and differences with other studies • Discuss unexpected or surprising results • Are there any specific theoretical implications or practical applications of

your results? • Summarize the evidence for your conclusions

Step 11: Dicussion

The abstract is a mini-version of your contribution. Take into consideration that most people will only read your abstract. So, do your best effort!

• Follow the same IMRAD structure than the entire

article • Concisely and clearly written in past tense (referring to

your work) • Focus on your most relevant results and conclusions • Restrict yourself to the word limit of the journal (often

100-300 words)

Step 12: Abstract

TIP: Do not hold back any important result or conclusion, because most people will only read your abstract!

Abstract writing sample This paper reports studies on the territorial behavior patterns shown by males of the dragonfly species Plathemis lydia at a small pond in the vicinity of Earlville, NY. A total of 51 male dragonflies were marked with small spots of enamel paint applied to the abdominal portion of the body and were observed under natural conditions during the month of June 2005. It was found that males showed a strong tendency to defend individual areas at the pond. These males chased away other males of their species, and also, on occasion, even males of other species of dragonflies. Threat behavior, as opposed

to behavior involving physical contact, was the most common aggressive behavior displayed by males defending their areas against intruders. Males typically remained at the same area of the pond for 2 h or longer on a single day. Also, they usually were observed returning to the same area on successive days. These observations suggest the possibility that male territorial behavior in this species serves the adaptive function of enabling the owners to monopolize particular areas. These areas may be visited by females who are in the act of seeking mates.

(McMillan 2006)

Eliminate repetitions and superfluent words

This paper reports studies on the territorial behavior patterns shown by males of the dragonfly species Plathemis lydia at a small pond in the vicinity of Earlville, NY. A total of 51 male dragonflies were marked with small spots of enamel paint applied to the abdomen al portion of the body and were observed under natural conditions during the month of June 2005. It was found that males showed a strong tendency to defend individual areas at the pond and. These males chased away other males of their species, and also, on occasion, even males of other species of dragonflies. Threat behavior, as opposed

to behavior involving physical contact, was the most common aggressive behavior displayed by males defending their areas against intruders. Males typically remained at the same area of the pond for 2 h or longer on a single day. Also, they usually were observed returning to the same area on successive days. These observations suggest the possibility that male territorial behavior in this species serves the adaptive function of enabling the owners to monopolize particular areas. These areas may be visited by females who are in the act of seeking mates.

(McMillan 2006)

Possible solution after rewriting I studied the territorial behavior of male dragonflies (Plathemis lydia) at a small pond near Earlville, NY. Fifty-one males were marked with enamel paint on the abdomen and observed under natural conditions during June 2005. Males defended individual areas from male conspecifics and occasionally from males of other species. Aggressive interaction generally involved threat behavior rather than physical contact. Territory owners typically remained at the same area for at least 2 h and returned to the same location on successive days. Territorial behavior in

this species may be adaptive for males, enabling them to monopolize areas likely to be visited by females seeking mates.

Abstract structure of this example Intro: I studied the territorial behavior of male dragonflies (Plathemis lydia) at a small pond near Earlville, NY. Method: Fifty-one males were marked with enamel paint on the abdomen and observed under natural conditions during June 2005. Results: Males defended individual areas from male conspecifics and occasionally from males of other species. Aggressive interaction generally involved threat behavior rather than physical contact. Territory owners typically remained at the same area for at least 2 h and returned to the same location on

successive days. Discussion: Territorial behavior in this species may be adaptive for males, enabling them to monopolize areas likely to be visited by females seeking mates.

Tips: Check structure

Clear aim of the study

Verify abstract length (author guidelines)

• Technical or logistic support provided by individuals or institutions

• Funding agencies (often obligatory!) • Grants, scholarships, fellowships (often

obligatory!) • Colleagues, who provided ideas, photographs,

maps, or reviewed different versions of the manuscript

• Anonymous (and known) reviewers and editors

Step 13: Acknowledgements

TIP: You have to obtain permission from each person to thank them in this section. They may consider the acknowledgment insufficient or exaggerated and unnecessary!

• Need to be formatted specifically for each journal • Common styles:

– Name/Year (Harvard system): e.g., Smith (2015) – Alphabet-Number : (7, 12) reference list at the end is

in alphabetic order – Citation order: (3, 4) reference list at the end is in

order of citation

• Check the right citation of unpublished work, work in press, comments, etc.

Step 14: References - Literature cited

TIP: Even if you use reference software such as Endnote, Mendeley or Reference Manager, double check the final output!

• Results should be presented in the text OR in tables OR figures

• Use figures and tables for significant and complex data. • If you can resume results in a single sentence, avoid

tables and figures. • Numeric values should run in columns, not in rows • Do not use vertical lines in tables • Use horizontal lines only on top and bottom of the

table and to separate column headings from your data • Typically, column headings are centered, text columns

are aligned to the left, number columns to the right.

Step 15: Tables and Figures

TIP: Use readable font sizes and symbols in your figures. Ensure that all axes have titles and SI units. Avoid too many abbreviations!

• Ask good colleagues to revise a complete version of your manuscript before submission to a journal.

• Their feedback will be kind, but professional. • They may find major flaws before you submit your

contribution. For instance: – Clarity of the aim of your study – Definition of specific terms you used throughout the

manuscript – Awkward, long winding sentences – Errors in calculations – Suggestions of other analyses

Step 16: Friendly review

TIP: Be a friendly reviewer for your colleagues and they will return the favor!

Many good research papers are not considered for publication because they contain many grammatical and orthographic errors in English, which affect the readability and clarity of your contribution. Consequently, reviewers and editors may judge your research not on merit alone, but the lack of professional standard of language. Improve your English proficiency: • Read English novels, not just scientific papers. • Visit English speaking countries. • Use electronic dictionaries, spellchecking and grammar software. Revise English: • Ask a native English-speaking colleague to revise your manuscript. • Send your manuscript to a professional editor of scientific English language. • Use professional language services for authors of Editorials or third parties. Reread your manuscript • Ensure that no fact was misinterpreted by the language editor.

Step 17: Language edition

TIP: Time is money. Language editors may charge higher fees for faster services!

Writing tools: Dictionaries/Manuals of style

Online resources www.springer.com

https://cgi.duke.edu/web/sciwriting/

http://writingcenter.tamu.edu/Home

Step 17: Language edition

Reasons for journal selection: • Research field (e.g., ecology, botany, aquatic botany,

hydrology) • Impact (e.g., impact factor), prestige • Rejection rate • Speed of review process and publication • Circulation, audience (e.g., specific society), visibility (e.g.,

citations) • Open Access • Publication fees

Step 18: Journal selection

TIP: Write your manuscript with the journal (and their readership) in mind! Try some helpful web applications such as Springer’s Journal Suggester, Edanz Journal Selector or Elsevier’s Journal Finder!

The manuscript format depends on the selected journal, editorial and type of contribution (e.g., orginal research, scientific note, review, etc.). Follow the author guidelines of your journal. • Common features: Font Times New Roman, size 12 pts, double-

spaced, left justified, without hyphenation, all margins 25-30 mm Format affects mainly: • Length of the entire manuscript and abstract • Style of abbreviations, periods, commas, italics • Style of references cited within the text of the manuscript and in

the references section • British or American English

Step 19: Manuscript formatting

TIP: Never resubmit a rejected contribution to another journal without reformatting your manuscript.

• Online electronic submission via manuscript central (or email) • Follow author guidelines • Provide text as word processor files, e.g. docx • Picture files may have size limits (10-20MB), often require a specific

resolution (300, 600 dpi) and must be provided in the required format (e.g., tif, gif)

• You may be asked – to suggest reviewers (no coauthors during the last 5 years) – to give a statement of no conflict (of interest) – to state that all authors approved final ms.

• Letter to the Editor

– Title/Original article/Type of contribution/nowhere else submitted – Explain main results/of interest for the chosen journal.

Step 20: Manuscript submission

In case your contribution was accepted with minor/major changes or you were invited to resubmit your rejected paper, you will send it once more to the same journal.

• Correct all marked errors. • Attend all suggestions raised by the reviewers and editors. • Justify clearly if you did not attend some of the suggestions. • Respond to all comments on a point-by-point basis, indicating the specific

location in the updated (and former) version of the manuscript: – E.g. Associate Editor: I suggest to avoid this technical term, because our broad

audience might be unfamiliar with these mycological details. • Page 7, Line 5: We kept the technical term, because it captures the specific

morphological feature discussed in our contribution. However, we added a short definition for the readership.

Step 21: Resubmission

TIP: Meet the deadline for resubmission of an accepted manuscript with minor/major changes or it will be considered a new submission!

• Once you receive a proof of your copyedited manuscript from the publisher, proofreading is your responsibility.

• Follow carefully the editorial instructions (e.g. proofreaders’ marks)

• Respond within the established deadline (often 48-72 hrs)

• If you wait for proofs, tell the journal in advance, if you will be unreachable for some time.

Step 22: Proofreading

• Watch out especially for misspelled words, technical terms, formulas, numbers and decimal points, quality of figures and tables and their corresponding legends, and the abstract.

• Be very clear and specific – Page 5, Line 6: “responsable” should be “responsible”

with an “i” – Table 2, Column “Height”, Line 2: Replace number

“12.8” with “1.8” • Avoid any substantial changes

– High fees for alterations made by authors

Step 22: Proofreading

TIP: Clearly state if you want to correct erroneous alterations made by the copyeditor, or you might be charged for them by the printer!

• Copyright agreement of all authors (If you have used material from other sources (e.g., books) you need to ask the copyright owner for permission!)

• Statement of no conflict • Fees:

– Page charges (e.g., (15-)40-60(-100)USD/page) – Publication fees (e.g., single fee, 300-1000 USD) – Printing costs for color plates (e.g. 2000 USD/plate) – Open Access fees (e.g. single fee, 1000-3000 USD)

• Self-archiving (on your website) • Data sharing (editorial, websites)

Step 23: Final acceptance

TIP: Ensure that you have the right to place a pdf file of your work on your website!

Data sharing

Self-archiving

http://www.sherpa.ac.uk/romeo/index.php

Self-archiving

What can you do to publish more? • Option 1: write in Spanish and

hire a professional to translate your manuscript

• Option 2: collaborate with a productive group of academics

• Option 3: amend your English proficiency by spending a year in the US or UK

• Option 4: read English books (I mean novels and non-fiction!)

Final advice • Purchase your own dictionary and manual of style. • Read as much as possible in English. • Practice: Schedule daily one hour for writing. • Do not be a perfectionist if you start writing, but:

Outline, draft, and plan to rewrite your manuscript several times.

• Talk with colleagues and coauthors about problems of writing and publishing.

• Be a perfectionist when formatting and submitting your paper.

Further reading

Winston Churchill

• Success consists of going from failure to failure without loss of enthusiasm.

Albert Einstein

• Anyone who has never made a mistake has never tried anything new.

Acknowledgments:

David Mouriño

Staff of Springer Nature

Dr. Klaus Mehltreter, Instituto de Ecología, A.C., Xalapa, kmehltreter@gmail.com